Abstract Background Pleural fluid pH has diagnostic, therapeutic, and prognostic implications in the management of pleural space infections and malignancy. Pleural fluid sample collection, transportation and processing are known for source of pre-analytical error which contribute to inaccuracy of measured pH with clinical implication to patient care. Some clinical practices observed locally include pleural fluid collection in sterile container for ease of other biochemistry analytes measurement in addition to pH. This study aimed to compare the differences in pleural fluid pH and other commonly ordered biochemistry analytes collected using sterile container against heparinized blood gas syringe. Methods Total 20 Pleural fluid samples were collected from patient using a procedure called thoracentesis from, with approximately 2 to 3ml of fluid directly transferred into heparinized blood gas syringe as well as in a sterile container. Both samples were then transported to Clinical Biochemistry Laboratory within an hour. Both samples were analyzed on 3 analytical systems; 1) pH on Roche COBAS b221 blood gas analyzer, 2) Glucose, Total Protein, LDH on Beckman AU System and 3) Specific Gravity on Reflectometer. Statistical analysis was performed using Analyze-It software. Results pH fluid collected in sterile container demonstrates significant high bias (absolute of 0.4 units or 5%) as compared to sample collected in heparinizes blood gas syringe. Other commonly ordered tests in fluid profile (Glucose, Total Protein, LDH and SG) demonstrate good correlation (Altman-Bland Difference Plot <5%) for pleural fluid collected in sterile container as compared to heparinized syringe. Conclusions This positive bias observed is likely attributed to air exposure in pleural fluid collection in sterile container as compared to heparinized syringe. The accuracy of measured pleural pH is critically dependent on the method of sample collection. This study highlights the need for a standardized protocol for pleural pH collection for accurate measurement.